Mercurial > repos > iuc > khmer

diff abundance-dist.xml @ 0:0187f18785a3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
author: iuc
date: Sat, 17 Oct 2015 04:02:33 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abundance-dist.xml	Sat Oct 17 04:02:33 2015 -0400
@@ -0,0 +1,69 @@
+<tool id="gedlab-khmer-abundance-dist" name="Abundance Distribution" version="@WRAPPER_VERSION@-4">
+    <description>
+        Calculate abundance distribution of the k-mers in a given sequence file using a pre-made k-mer countgraph
+    </description>
+    <macros>
+        <token name="@BINARY@">abundance-dist.py</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version" />
+    <command><![CDATA[
+set -xu &&
+mkdir output && cd output &&
+@BINARY@
+--squash
+${zero}
+${bigcount}
+${input_countgraph_filename}
+${input_sequence_filename}
+${output_histogram_filename}
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_countgraph_filename" />
+        <expand macro="input_sequence_filename" />
+        <expand macro="input_zero" />
+        <expand macro="input_bigcount" />
+    </inputs>
+    <outputs>
+        <expand macro="abundance-histogram-output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
+            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
+            <param name="zero" value="false" />
+            <output name="output_histogram_filename">
+                <assert_contents>
+                    <has_text text="1,96,96,0.98" />
+                    <has_text text="1001,2,98,1.0" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_sequence_filename" value="test-abund-read-2.fa" />
+            <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
+            <param name="zero" value="false" />
+            <param name="bigcount" value="false" />
+            <output name="output_histogram_filename">
+                <assert_contents>
+                    <has_text text="1,96,96,0.98" />
+                    <has_text text="255,2,98,1.0" />
+                    </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Calculate abundance distribution of the k-mers in the sequence file using a
+pre-made k-mer countgraph.
+
+@HELP_FOOTER@
+]]>
+    </help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="counting-citation" />
+    </citations>
+</tool>